The indexed Iranian journals in ISI and PubMed at the end of 2012 with known impact factor (IF) were evaluated with regard to the number of articles published in 2010-2012, the number of citations by authors from inside and outside Iran, their IF as well as their ranking order among all other journals in their specialized categories. There were among 130 English journals, 21 indexed with known IF. The mean IF of these journals increased from 0.4 in 2010 to 0.68 in 2012. The number of citations per article by authors from outside Iran increased from 0.19 to 0.49 during the same time period. The rank of the majority of the indexed journals was in the lowest 20% of their category. Although some improvement has been observed in the quality and the number of citations of Iranian journals indexed in ISI during these two years, the quality of the manuscripts remains low. A reduction in the number of journals, a change of their structure as well as more financial resources for research is necessary for the improvement of the quality and better rank and status of Iranian science among an international audience.